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8/3/2019 One Java Project 2 Different Views 6
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The Project is AcidMiner: but what is that?
How did it go
Project Results
Technical Observations and Lessons
Lessons and Conclusion
Question and Answers
What is AcidMiner
How did it go
Project Results
Technical Observations and Lessons
Lessons and Conclusion
Q&A
Quick Ref Blob:Genome is the entire set of genes
(and everything in between)
in an organism;Evolutionarily family tree of species is
called a phylogeny.
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Quick Ref Blob:Proteins are made out of 20 kinds of
monomers called amino acids;
Evolutionarily related proteins are called homologs;Most evolutionary changes occur by amino acid
substitutions (1 at a time).
L
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OR
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Outgroup
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Genome-wide
phylogenetic
reconstruction of amino
acid substitutions using
triplets of genomes is
routine, but using the
whole phylogenyinformation is not trivial
What is AcidMiner
How did it go
Technical Observations and Lessons
Project Results
Lessons and Conclusion
Q&A
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Onlinedatabase at
Indiana State
University
OtherSources
Manual Feed
Java Code
CachDMBS
JDBC/ODBC
SQL
Results
???
StatisticalSoftware
TableswithAggregates
???
What is AcidMiner
How did it go
Project Results
Technical Observations and Lessons
Lessons and Conclusion
Q&A
8/3/2019 One Java Project 2 Different Views 6
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Onlinedatabase at
Indiana State
University
OtherSources
Java Code
GeneOntology,etc
Manual Feed
Results
Excel(Oops)
TableswithAggregates
CachDMBS
DBVisualizer(SQL)
Export to Flat
Files (CSV,XLS)
SQL(DBVisualizer)
StatisticalSoftware
(JMP)
Manual
Semi-Automatic
data Retrieval
In-DatabaseCalculations
(DerivativeProcessing)
Results: Fluxes in Amino acid substitutions
Frequencies are far from an
equilibrium: frequent aminoacids are losers, rare are
gainers (so frequencies are ontheir way to an equilibrium)
Consistent with Jordan et al.,Nature 2005.
Most proteins lose average
polarity compared to the
ancestral state. This effect isthe strongest in intracellular,
and the weakest in membraneproteins.
Rela
tive
loss
/gai n
Project Results Project Results
Remaining copy
conserved
One copy conserved,
the other underpositive selection
Both copiesconserved
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Project Results
Yes, in most functional classes (except transporters)
Project Results
Yes, in numerous gene families, indicating widespread
neofunctionalization.
Caveat: some may be a signature of retained pseudogene.
Asymmetryparameter
Number ofduplications
tested
Clade asymmetry,FDR = 0.05
Clade asymmetry,Bonferroni-
adjusted P< 0.05
Number ofsubstitutions
4646 1770 905
|DPolarity| 2951 179 39
What is AcidMiner
How did it go
Project Results
Technical Observations and Lessons
Lessons and Conclusion
Q&A
8/3/2019 One Java Project 2 Different Views 6
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9/25/10
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What is AcidMiner
How did it go
Project Results
Technical Observations and Lessons
Lessons and Conclusion
Q&A
8/3/2019 One Java Project 2 Different Views 6
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9/25/10
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What is AcidMiner
How did it go
Technical Observations and Lessons
Project Results
Lessons and Conclusion
Q&A